How these Anti viruses are working....

As far as I can remember, my cousin told me that some viruses can destroy your computer if you try to delete them manually. Some antivirus programs also make some questionable searches done by them. I even had this incident where my brother's file, WaffleRO.exe was categorized as a virus together with another file used to execute the said .exe file. I just got confused but I still let the antivirus remove the programs.